The purpose of this function is to suggest custom primer experiments to
extend and "double strand" contigs. First the routine finds regions of
contigs with data on only one strand. Then it selects templates and
primers, which if used in sequencing experiments, would produce data to
cover these single stranded regions. This information is written to a
file or a list and also appears in the Output window. For each primer
suggested a tag is automatically created containing the template name
and the sequence. See also section Suggest Long Readings, and
section Double Stranding.

The following example shows how the results appear in the Output
window.

The contigs to process can be a particular
"single" contig, "all contigs", or a subset of contigs whose names are
stored in a "file" or a "list". If a file or list is selected the
browse button will be activated and, if it is clicked, an appropriate
browser will be invoked. If the user selects "single", then the
dialogue for choosing the contig and the section to process becomes
active.

The primer sequences, their template names and their reading names can
be written to a file or a list and an appropriate browser can be used to
aid its selection.

For each single stranded region located, the program will search for a
primer on its 5' side in the region "search start position", to
"search end position". That is, it will try to locate a primer starting at
"search start position" and then will look increasingly further away
until it reaches "search end position".

If required, by employing the "number of primers per match" entry box,
the user can request that the program tries to suggest more than one
primer per problem. The "primer start number" is an attempt to
generate a unique name for each primer suggested. If the number was
set to, say 11, and the database was named B0334, then the first primer
would be named B0334.11, the next B0334.12, etc in the output file.

The "Edit parameters" button invokes a dialogue box which allows the
specification of further parameters. Primer constraints can be specified
by melting temperature, length and G+C content.

This page is maintained by
James Bonfield.
Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_109.html